gene.select.FC: Function to select genes according to fold change

In MAMA: Meta-Analysis of MicroArray

Description

Function selects genes with fold change (in absolute value) above input cutoff

Usage

gene.select.FC(fch, cutoff)

Arguments

fch	Data frame of fold change with columns corresponding to microarray experiments and rows to genes
cutoff	Cutoff for selection

Value

List - each slot refers to one column of input data frame and it is a vector of genes names with fold change above selected threshold

Author(s)

Ivana Ihantova

Examples

#data preparation
data(Singhdata)
cl1<-as.data.frame(Singhdata$classes[[1]])
names(cl1)<-"classlab"
cl2<-as.data.frame(Singhdata$classes[[2]])
names(cl2)<-"classlab"
cl3<-as.data.frame(Singhdata$classes[[3]])
names(cl3)<-"classlab"

rownames(Singhdata$esets[[1]])<-Singhdata$geneNames
rownames(Singhdata$esets[[2]])<-Singhdata$geneNames
rownames(Singhdata$esets[[3]])<-Singhdata$geneNames

dataset<-new("MetaArray", GEDM=list(Singhdata$esets[[1]], Singhdata$esets[[2]], Singhdata$esets[[3]]),
clinical=list(cl1, cl2, cl3), datanames=c("dataset1", "dataset2", "dataset3"))

#fold change
fch<-fold.change(dataset, "classlab")
#gene selection
genes.selected<-gene.select.FC(fch, 1)

MAMA documentation built on Jan. 15, 2017, 3:05 p.m.